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Development of detection schemes for endangered and invasive animals based on pan-animalia enviromental DNA analysis

Research Project

Project/Area Number 17K19298
Research Category

Grant-in-Aid for Challenging Research (Exploratory)

Allocation TypeMulti-year Fund
Research Field Forestry and Forest Products Science, Applied aquatic science, and related fields
Research InstitutionUniversity of the Ryukyus

Principal Investigator

SATO Yukuto  琉球大学, 戦略的研究プロジェクトセンター, 特命講師 (20566418)

Project Period (FY) 2017-06-30 – 2019-03-31
Project Status Completed (Fiscal Year 2018)
Budget Amount *help
¥6,500,000 (Direct Cost: ¥5,000,000、Indirect Cost: ¥1,500,000)
Fiscal Year 2018: ¥3,640,000 (Direct Cost: ¥2,800,000、Indirect Cost: ¥840,000)
Fiscal Year 2017: ¥2,860,000 (Direct Cost: ¥2,200,000、Indirect Cost: ¥660,000)
Keywords環境DNA / 大量DNA分析 / 次世代シークエンサー / バイオインフォマティクス / 希少種 / 外来種 / メタバーコーディング / 遺伝的多様性 / 生態調査
Outline of Final Research Achievements

Methodological aspects of environmental DNA (eDNA) metabarcoding for vertebrates were investigated to detect tetrapods (amphibians, reptiles, avians, and mammals) from water samples. Using the Okinawa Island of Japan as a model system, I improved methods of water filtering, sample preservation, polymerase chain reaction (PCR) including choice of DNA polymerases and annealing temperatures, and data analysis. As a result, I achieved to detect eDNAs of endangered and invasive species of Okinawa Island which included Oryzias latipes, Babina holsti, Gallirallus okinawae, Poecilia reticulata, and Trachemys scripta. In addition, I showed that potential host animals of zoonotic pathogen Leptospira could be estimated based on the developed eDNA metabarcoding methods of river waters through correlated detection of pathogen bacterium and co-occurring vertebrate species.

Academic Significance and Societal Importance of the Research Achievements

本研究によって、河川水や海水から脊椎動物(魚類・四足類)の生息を検出する環境DNAメタバーコーディングの手法面が改良されたことで、環境DNA解析を、従来主な対象とされてきた魚類だけでなく、広く脊椎動物一般の検出と研究に活用していける可能性が示された。また本研究は、この環境DNA解析法を、人獣共通感染症の病原体の宿主となっている動物種の推定にも応用し得ることを論文成果として示した。今回、希少種や外来種を含む様々な脊椎動物を環境DNAで検出できたことを踏まえて、今後は検出の定量性や感度などを改良し、さらに遺伝的多様性推定の実現も目指すことで、保全生物学やメタ遺伝解析へ応用していくことが期待される。

Report

(3 results)
  • 2018 Annual Research Report   Final Research Report ( PDF )
  • 2017 Research-status Report
  • Research Products

    (14 results)

All 2019 2018 2017

All Journal Article (6 results) (of which Int'l Joint Research: 1 results,  Peer Reviewed: 6 results,  Open Access: 3 results,  Acknowledgement Compliant: 1 results) Presentation (8 results) (of which Invited: 2 results)

  • [Journal Article] Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan2019

    • Author(s)
      Yukuto Sato, Masaru Mizuyama, Megumi Sato, Toshifumi Minamoto, Ryosuke Kimura, Claudia Toma
    • Journal Title

      Scientific Reports

      Volume: 9(6575) Issue: 1 Pages: 1-11

    • DOI

      10.1038/s41598-019-42978-1

    • NAID

      120006891158

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access / Int'l Joint Research
  • [Journal Article] MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding2018

    • Author(s)
      Yukuto Sato, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, Wataru Iwasaki
    • Journal Title

      Molecular Biology and Evolution

      Volume: 35 Issue: 6 Pages: 1553-1555

    • DOI

      10.1093/molbev/msy074

    • Related Report
      2018 Annual Research Report
    • Peer Reviewed / Open Access
  • [Journal Article] Comparing local‐ and regional‐scale estimations of the diversity of stream fish using eDNA metabarcoding and conventional observation methods2018

    • Author(s)
      Hikaru Nakagawa, Satoshi Yamamoto, Yukuto Sato, Tetsuya Sado, Toshifumi Minamoto, and Masaki Miya
    • Journal Title

      Freshwater Biology

      Volume: February 2018 Issue: 6 Pages: 1-1

    • DOI

      10.1111/fwb.13094

    • NAID

      120006463755

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding2018

    • Author(s)
      Yukuto Sato, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, and Wataru Iwasaki
    • Journal Title

      Molecular Biology and Evolution

      Volume: in press Pages: 1-1

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Environmental DNA enables detection of terrestrial mammals from forest pond water2017

    • Author(s)
      Masayuki Ushio, Hisato Fukuda, Toshiki Inoue, Kobayashi Makoto, Osamu Kishida, Keiichi Sato, Koichi Murata, Masato Nikaido, Tetsuya Sado, Yukuto Sato, Masamichi Takeshita, Wataru Iwasaki, Hiroki Yamanaka, Michio Kondoh, and Masaki Miya
    • Journal Title

      Molecular Ecology Resources

      Volume: 17(6):e Issue: 6 Pages: 63-75

    • DOI

      10.1111/1755-0998.12690

    • Related Report
      2017 Research-status Report
    • Peer Reviewed
  • [Journal Article] Environmental DNA metabarcoding reveals local fish communities in a species-rich coastal sea2017

    • Author(s)
      Yamamoto, Masuda, Sato, Sado, Araki, Kondoh, Minamoto, Miya
    • Journal Title

      Scientific Reports

      Volume: 7 Issue: 1 Pages: 40368-40368

    • DOI

      10.1038/srep40368

    • NAID

      120005947171

    • Related Report
      2017 Research-status Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Presentation] IIBMP2018 生命情報科学若手の会 ハイライトトラック: MitoFish and MiFish pipeline: a mitochondrial genome database of fish with an analysis pipeline for environmental DNA metabarcoding.2018

    • Author(s)
      Yukuto Sato, Masaki Miya, Tsukasa Fukunaga, Tetsuya Sado, Wataru Iwasaki
    • Organizer
      第7回生命医薬情報学連合大会
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] Isolation of environmental pathogenic Leptospira from soil collected in the northern part of Okinawa.2018

    • Author(s)
      Idam Hermawan, Chiaki Matsuura, Yukuto Sato, Claudia Toma
    • Organizer
      第71回日本細菌学会九州支部総会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 沖縄県における土壌からの病原性レプトスピラの分離2018

    • Author(s)
      Idam Hermawan、松浦千晶、佐藤 行人、山城哲、トーマ・ クラウディア
    • Organizer
      第59回日本熱帯医学会大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] 環境DNA解析による種内の遺伝的変異性評価の試み-ウミヘビ類を例として2018

    • Author(s)
      徳山孟伸・佐藤行人・笹井隆秀・戸田守
    • Organizer
      日本爬虫両棲類学会・第57回大会
    • Related Report
      2018 Annual Research Report
  • [Presentation] Preliminary study on eDNA of the coelacanth's habitat around deep sea conservation areas of North Sulawesi, Indonesia2018

    • Author(s)
      Kawilarang W.A. Masengi, I.F. Mandagi, H. Manengkey, P.N.I. Kalangi, A. Luasunaung, F.P.T. Pangalila, M. Iwata, Y. Abe, Y. Sato, R. Kimura, K. Yamahira
    • Organizer
      第10回世界水族館会議
    • Related Report
      2018 Annual Research Report
    • Invited
  • [Presentation] 沖縄県北部におけるレプトスピラ環境DNAに関する研究2018

    • Author(s)
      水山 克,佐藤行人, サトウ 恵,源 利文,トーマ クラウディア
    • Organizer
      第55回レプトスピラ・シンポジウム
    • Related Report
      2017 Research-status Report
  • [Presentation] ウミヘビ類を対象とした環境 DNA 分析の有効性の評価2017

    • Author(s)
      徳山孟伸,佐藤行人,笹井隆秀,戸田 守
    • Organizer
      沖縄生物学会第54回大会
    • Related Report
      2017 Research-status Report
  • [Presentation] Development of environmental DNA (eDNA) analysis platform in the University of the Ryukyus2017

    • Author(s)
      Yukuto Sato, Kaori Tsurui-Sato, Shingo Fujimoto
    • Organizer
      OIST and Unv. Ryukyus Joint Symposium 2017, OIST Auditorium & Conference Center, Onna-son, Okinawa, October 31, 2017
    • Related Report
      2017 Research-status Report

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Published: 2017-07-21   Modified: 2020-03-30  

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